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Assessing the quality in specific regions of a model
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  International Tables for Crystallography (2012). Vol. F, Section 21.2.3.1.3.2, pp. 670-673 [ doi:10.1107/97809553602060000880 ]
Assessing the quality in specific regions of a model 21.2.3.1.3.2. Assessing the quality in specific regions of a model The main purpose for computing the four local quality measures, the B factor, the Density index, the atomic displacement (Shift) and the Density correlation (Table 21.2.3.3), is to identify problem regions in ...
     [more results from section 21.2.3 in volume F]

Deviations from standard atomic volumes as a quality measure for protein crystal structures
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  International Tables for Crystallography (2012). Vol. F, Section 21.2.2.2.3, pp. 664-665 [ doi:10.1107/97809553602060000880 ]
... ranges could be readily derived. References Abagyan, R. A. & Totrov, M. M. (1997). Contact area difference (CAD): a robust measure to ... procedure. J. Mol. Biol. 161, 305-322. Harpaz, Y., Gerstein, M. & Chothia, C. (1994). Volume changes on protein folding. ...
     [more results from section 21.2.2 in volume F]

Introduction
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  International Tables for Crystallography (2012). Vol. F, Section 21.2.1, p. 662 [ doi:10.1107/97809553602060000880 ]
... the model with the data. References Laskowski, R. A., MacArthur, M. W. & Thornton, J. M. (1998). Validation of protein models derived from experiment. Curr. Opin. Struct. Biol. 8, 631-639. MacArthur, M. W., Laskowski, R. A. & Thornton, J. M. (1994). ...

Concluding remarks
Wodak, S. J., Vagin, A. A., Richelle, J., Das, U., Pontius, J. and Berman, H. M.  International Tables for Crystallography (2012). Vol. F, Section 21.2.5, p. 673 [ doi:10.1107/97809553602060000880 ]
... the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey, pp. 11-22. Warrington: Daresbury Laboratory. Das, U., Chen, S., Fuxreiter, M., Vaguine, A. A., Richelle, J., Berman, H. M. & Wodak, S. J. (2001). Checking nucleic ...

SUB_CATEGORY_EXAMPLES
Westbrook, J. D., Berman, H. M. and Hall, S. R.  International Tables for Crystallography (2006). Vol. G, Section 2.6.6.2.8, p. 70 [ doi:10.1107/97809553602060000732 ]
SUB_CATEGORY_EXAMPLES 2.6.6.2.8. SUB_CATEGORY_EXAMPLES The DDL category SUB_CATEGORY_EXAMPLES holds examples of a subcategory. A subcategory example might illustrate valid instances of the items comprising the subcategory. An example specification contains the text of the example, _sub_category_examples.case, and an optional comment item, _sub_category_examples.detail ...
     [more results from section 2.6.6 in volume G]

Supporting software
Westbrook, J. D., Henrick, K., Ulrich, E. L. and Berman, H. M.  International Tables for Crystallography (2006). Vol. G, Section a3.6.2.4, p. 197 [ doi:10.1107/97809553602060000738 ]
Supporting software A3.6.2.4. Supporting software The RCSB/PDB has developed a set of software tools which support the PDB exchange dictionary framework (Chapter 5.5 ). These include PDB_EXTRACT, a tool to extract data from the output files of structure determination applications; ADIT, a web-based editor for data files based ...

Protein production
Westbrook, J. D., Henrick, K., Ulrich, E. L. and Berman, H. M.  International Tables for Crystallography (2006). Vol. G, Section a3.6.2.3.3, p. 197 [ doi:10.1107/97809553602060000738 ]
Protein production A3.6.2.3.3. Protein production The International Task Force on Deposition, Archiving, and Curation of Primary Information for Structural Genomics (Section A3.6.2.2) has also provided recommendations for the deposition of information about protein production. These recommendations are summarized at http://deposit.pdb.org/mmcif/sg-data/protprod.html . These data extensions have been ...

Cryo-electron microscopy
Westbrook, J. D., Henrick, K., Ulrich, E. L. and Berman, H. M.  International Tables for Crystallography (2006). Vol. G, Section a3.6.2.3.2, p. 197 [ doi:10.1107/97809553602060000738 ]
... mmcif_iims.dic/Index/ ). References Henrick, K., Newman, R., Tagari, M. & Chagoyen, M. (2003). EMDep: a web-based system for the deposition ...

NMR
Westbrook, J. D., Henrick, K., Ulrich, E. L. and Berman, H. M.  International Tables for Crystallography (2006). Vol. G, Section a3.6.2.3.1, p. 197 [ doi:10.1107/97809553602060000738 ]
NMR A3.6.2.3.1. NMR The PDB exchange dictionary includes a description of NMR sample preparation, structure solution methodology, refinement and refinement metrics. These extensions were developed in collaboration with the BioMagResBank (BMRB; Ulrich et al., 1989). The BMRB is the archive for experimental NMR data for biological macromolecules and has played ...

Noncrystallographic methods
Westbrook, J. D., Henrick, K., Ulrich, E. L. and Berman, H. M.  International Tables for Crystallography (2006). Vol. G, Section a3.6.2.3, p. 197 [ doi:10.1107/97809553602060000738 ]
... Comput. Sci. 31, 326-333. Henrick, K., Newman, R., Tagari, M. & Chagoyen, M. (2003). EMDep: a web-based system for the deposition ...

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